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Motif finding is one of the NP-complete problems in Computational Biology. Existing nondeterministic algorithms for motif finding do not guarantee the global optimality of results and are sensitive to initial parameters. To address this…

Distributed, Parallel, and Cluster Computing · Computer Science 2016-05-24 Jhoirene B. Clemente , Francis George C. Cabarle , Henry N. Adorna

Homomorphic Encryption (HE) is an emerging encryption scheme that allows computations to be performed directly on encrypted messages. This property provides promising applications such as privacy-preserving deep learning and cloud…

Cryptography and Security · Computer Science 2021-10-01 Yujia Zhai , Mohannad Ibrahim , Yiqin Qiu , Fabian Boemer , Zizhong Chen , Alexey Titov , Alexander Lyashevsky

Simulations of physical phenomena are essential to the expedient design of precision components in aerospace and other high-tech industries. These phenomena are often described by mathematical models involving partial differential equations…

Computational Physics · Physics 2017-01-05 Daniel Magee , Kyle E Niemeyer

GPUs are playing an increasingly important role in general-purpose computing. Many algorithms require synchronizations at different levels of granularity in a single GPU. Additionally, the emergence of dense GPU nodes also calls for…

Distributed, Parallel, and Cluster Computing · Computer Science 2020-04-14 Lingqi Zhang , Mohamed Wahib , Haoyu Zhang , Satoshi Matsuoka

We present a fast, scalable, data-driven approach for solving relaxations of 0-1 integer linear programs. We use a combination of graph neural networks (GNN) and the Lagrange decomposition based algorithm FastDOG (Abbas and Swoboda 2022b).…

Machine Learning · Computer Science 2024-01-01 Ahmed Abbas , Paul Swoboda

Paraxial diffraction modeling based on the Fourier transform has seen widespread implementation for simulating the response of a diffraction-limited optical system. For systems where the paraxial assumption is not sufficient, a class of…

GPU architectures have become popular for executing general-purpose programs. Their many-core architecture supports a large number of threads that run concurrently to hide the latency among dependent instructions. In modern GPU…

Hardware Architecture · Computer Science 2024-01-19 Rodrigo Huerta , Mojtaba Abaie Shoushtary , Antonio González

This work arises on the environment of the ExaNeSt project aiming at design and development of an exascale ready supercomputer with low energy consumption profile but able to support the most demanding scientific and technical applications.…

Instrumentation and Methods for Astrophysics · Physics 2019-11-01 David Goz , Sara Bertocco , Luca Tornatore , Giuliano Taffoni

The Particle-In-Cell (PIC) method is a computational technique widely used in plasma physics to model plasmas at the kinetic level. In this work, we present our effort to prepare the semi-implicit energy-conserving PIC code ECsim for…

Disaggregation maps parts of an AI workload to different types of GPUs, offering a path to utilize modern heterogeneous GPU clusters. However, existing solutions operate at a coarse granularity and are tightly coupled to specific model…

Distributed, Parallel, and Cluster Computing · Computer Science 2026-04-14 Tiancheng Hu , Jin Qin , Zheng Wang , Junhao Hu , Yuzheng Wang , Lei Chen , Yizhou Shan , Mingxing Zhang , Ting Cao , Chunwei Xia , Huimin Cui , Tao Xie , Chenxi Wang

Recent hardware-aware matrix-free algorithms for higher-order finite-element (FE) discretized matrix-vector multiplications reduce floating point operations and data access costs compared to traditional sparse matrix approaches. This work…

Computational Physics · Physics 2024-12-31 Gourab Panigrahi , Nikhil Kodali , Debashis Panda , Phani Motamarri

Structural clustering is one of the most popular graph clustering methods, which has achieved great performance improvement by utilizing GPUs. Even though, the state-of-the-art GPU-based structural clustering algorithm, GPUSCAN, still…

Databases · Computer Science 2023-12-01 Long Yuan , Zeyu Zhou , Xuemin Lin , Zi Chen , Xiang Zhao , Fan Zhang

In high-performance computing, hotspot GPU kernels are primary bottlenecks, and expert manual tuning is costly and hard to port. Large language model methods often assume kernels can be compiled and executed cheaply, which fails in large…

Distributed, Parallel, and Cluster Computing · Computer Science 2025-12-30 Ruifan Chu , Anbang Wang , Xiuxiu Bai , Shuai Liu , Xiaoshe Dong

Although Federated Learning has been widely studied in recent years, there are still high overhead expenses in each communication round for large-scale models such as Vision Transformer. To lower the communication complexity, we propose a…

Machine Learning · Computer Science 2026-04-21 Junkang Liu , Fanhua Shang , Yuanyuan Liu , Hongying Liu , Yuangang Li , YunXiang Gong

This work presents a novel three-dimensional Crack Element Method (CEM) designed to model transient dynamic crack propagation in quasi-brittle materials efficiently. CEM introduces an advanced element-splitting algorithm that enables…

Computational Engineering, Finance, and Science · Computer Science 2025-08-07 Yuxi Xie , C. T. Wu , Wei Hu , Lu Xu , Tinh Q. Bui , Shaofan Li

Fully homomorphic encryption (FHE) has recently attracted significant attention as both a cryptographic primitive and a systems challenge. Given the latest advances in accelerated computing, FHE presents a promising opportunity for…

The strategy of using CUDA-compatible GPUs as a parallel computation solution to improve the performance of programs has been more and more widely approved during the last two years since the CUDA platform was released. Its benefit extends…

Distributed, Parallel, and Cluster Computing · Computer Science 2010-01-12 Chang Xu , Steven R. Kirk , Samantha Jenkins

In this paper, we present CT-AGD (Curvature-Tuned Accelerated Gradient Descent), an optimization method for non-convex optimization problems in deep learning training tasks. CT-AGD is a general boosting procedure that accelerates…

Machine Learning · Computer Science 2026-05-18 Manuel Graca , L. Miguel Silveira , Arlindo Oliveira , Frank Liu

In this paper, we address a long-standing challenge: how to achieve both efficiency and scalability in solving semidefinite programming problems. We propose breakthrough acceleration techniques for a wide range of low-rank…

Optimization and Control · Mathematics 2024-08-27 Qiushi Han , Zhenwei Lin , Hanwen Liu , Caihua Chen , Qi Deng , Dongdong Ge , Yinyu Ye

Dataset deduplication is widely recognized as a crucial preprocessing step that enhances data quality and improves the performance of large language models. A commonly used method for this process is the MinHash Locality-Sensitive Hashing…

Computation and Language · Computer Science 2026-05-19 Youngjun Son , Chaewon Kim , Jaejin Lee